Research workbench
Bacteroides ovatus GH5 xyloglucanase in complex with a xxxg heptasaccharide
Analyse Bacteroides ovatus GH5 xyloglucanase in complex with a xxxg heptasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZMR
- Type
- protein
- Length
- 931 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulase (glycosyl hydrolase family 5)
- EC
- 3.2.1.151
- UniProt
- A7LXT7
- Ligands
- BGC, XYS, GLO, GLC
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulase (glycosyl hydrolase family 5) (EC 3.2.1.151) | protein | 469 | 32% helix, 21% strand | A7LXT7 |
| B | Cellulase (glycosyl hydrolase family 5) (EC 3.2.1.151) | protein | 462 | 31% helix, 21% strand | A7LXT7 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 7 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 6 copies · chains A, B
- GLO · D-glucose · sugar · chains B
- GLC · alpha-D-glucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.57 | 0.74 | 52 | BTB, EDO |
| 2 | 288 | 0.55 | 0.76 | 48 | BGC, XYS, EDO, GLC |
| 3 | 126 | 0.47 | 0.78 | 21 | EDO |
| 4 | 200 | 0.45 | 0.74 | 23 | empty |
| 5 | 135 | 0.45 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 430 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ZMR · Bacteroides ovatus GH5 xyloglucanase in complex with a XXXG heptasaccharide · the same entry in another collection · chain A against A, TM-score 1.00
- A7LXT7 · AlphaFold monomer V2.0 prediction for xyloglucan-specific endo- beta-1,4-glucanase BOGH5A… · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A7LXT7
- Elsewhere: RCSB PDB 3ZMR · PDBe 3ZMR · UniProt A7LXT7
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